API Sample

API - Sample

The following is an example of the JSON returned for a sample, with the fields being documented after this section:

{
  "sample": {
    "actions": {
      "read": "http://www.example.com/api/1/00000000-1111-2222-3333-444444444444",
      "update": "http://www.example.com/api/1/00000000-1111-2222-3333-444444444444"
    },
    "sample_tubes": {
      "actions": {
        "read": "http://www.example.com/api/1/00000000-1111-2222-3333-444444444444/sample_tubes"
      }
    },

    "uuid": "00000000-1111-2222-3333-444444444444",

    "sanger": {
      "name": "testing_the_api",
      "sample_id": null,
      "resubmitted": null,
      "description": "sample_description"
    },
    "supplier": {
      "sample_name": "supplier_name",
      "storage_conditions": "sample_storage_conditions",

      "collection": {
        "date": "date_of_sample_collection"
      },
      "extraction": {
        "date": "date_of_sample_extraction",
        "method": "sample_extraction_method"
      },
      "purification": {
        "purified": "sample_purified",
        "method": "purification_method"
      },
      "measurements": {
        "volume": "volume",
        "concentration": "concentration",
        "gc_content": "Neutral",
        "gender": "Male",
        "concentration_determined_by": "concentration_determined_by"
      }
    },
    "source": {
      "dna_source": "Genomic",
      "cohort": "cohort",
      "country": "country_of_origin",
      "region": "geographical_region",
      "ethnicity": "ethnicity",
      "control": null
    },
    "family": {
      "mother": "mother",
      "father": "father",
      "replicate": "replicate",
      "sibling": "sibling"
    },
    "taxonomy": {
      "id": null,
      "strain": "sample_strain_att",
      "common_name": "sample_common_name",
      "organism": "organism"
    },
    "reference": {
      "genome": null
    },
    "data_release": {
      "visibility": "Hold",
      "public_name": "sample_public_name",
      "description": "sample_description",

      "metagenomics": {
        "genotype": "genotype",
        "phenotype": "phenotype",
        "age": "10 minutes",
        "developmental_stage": "developmental_stage",
        "cell_type": "cell_type",
        "disease_state": "disease_state",
        "compound": "compound",
        "dose": "10 something",
        "immunoprecipitate": "immunoprecipitate",
        "growth_condition": "growth_condition",
        "rnai": "rnai",
        "organism_part": "organism_part",
        "time_point": "time_point",
        "treatment": "treatment",
        "subject": "subject",
        "disease": "disease"
      },
      "managed": {
        "treatment": "treatment",
        "subject": "subject",
        "disease": "disease"
      }
    }
  }
}

All of the fields present within the sample element can be assumed to be read-write except for those marked below as read-only. To create or update samples please read the sample manifest section of this documentation.

sanger section

This section holds the information relevant to the institute.

• sanger.name (read-only)
• sanger.sample_id (read-only)
• sanger.resubmitted
• sanger.description

supplier section

Holds the information that the supplier is providing.

• supplier.sample_name
• supplier.storage_conditions
• supplier.collection.date
• supplier.extraction.date
• supplier.extraction.method
• supplier.purification.purified
• supplier.purification.method
• supplier.measurements.volume numeric value in micro litres
• supplier.measurements.concentration numeric value in nanograms
• supplier.measurements.gc_content one of Neutral, High AT, or High GC
• supplier.measurements.gender one of Male, Female, Mixed, Hermaphrodite, Unknown, or Not Applicable
• supplier.measurements.concentration_determined_by

source section

• source.dna_source one of Genomic, Whole Genome Amplified, Blood, Cell Line, Saliva, or Brain
• source.cohort
• source.country
• source.region
• source.ethnicity
• source.control

family section

• family.mother
• family.father
• family.replicate
• family.sibling

taxonomy section

• taxonomy.id
• taxonomy.strain
• taxonomy.common_name
• taxonomy.organism

reference section

• reference.genome

## data_release section Fields in this section control the data release of the sample information. Not all of them need to be provided, especially if you are only interested in the metagenomics or managed data release.

• data_release.accession_number
• data_release.sample_type
• data_release.visibility one of Hold, Public, or Protect (read-only)
• data_release.public_name
• data_release.description
• data_release.metagenomics.genotype
• data_release.metagenomics.phenotype
• data_release.metagenomics.age
• data_release.metagenomics.developmental_stage
• data_release.metagenomics.cell_type
• data_release.metagenomics.disease_state
• data_release.metagenomics.compound
• data_release.metagenomics.dose
• data_release.metagenomics.immunoprecipitate
• data_release.metagenomics.growth_condition
• data_release.metagenomics.rnai
• data_release.metagenomics.organism_part
• data_release.metagenomics.time_point
• data_release.metagenomics.treatment
• data_release.metagenomics.subject
• data_release.metagenomics.disease
• data_release.managed.treatment
• data_release.managed.subject
• data_release.managed.disease